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update annotation docs #668

Merged
merged 10 commits into from
Jul 20, 2022
Merged

update annotation docs #668

merged 10 commits into from
Jul 20, 2022

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maxulysse
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PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jul 20, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 44fb6d5

+| ✅ 146 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_description - No description provided in schema for parameter: ascat_ploidy

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-20 13:41:11

maxulysse
maxulysse commented Jul 20, 2022
View reviewed changes
conf/test_full.config
Comment on lines -22 to -23
genome = 'GATK.GRCh38'
schema_ignore_params = 'genomes'
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@ggabernet removing that because we don't need it actually

maxulysse
maxulysse commented Jul 20, 2022
View reviewed changes
conf/test_full_somatic.config
Comment on lines -22 to -23
genome = 'GATK.GRCh38'
schema_ignore_params = 'genomes'
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@ggabernet same here

@FriederikeHanssen FriederikeHanssen mentioned this pull request Jul 20, 2022
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@FriederikeHanssen FriederikeHanssen merged commit ce77595 into nf-core:dev Jul 20, 2022
@maxulysse maxulysse deleted the dev_annotation_docs branch July 20, 2022 14:21
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen